v1.9.1 - Nice Nieuwkerke

Changes

1. Updated the ROI file in the WES profile from v5 to v6

v1.9.0 - Neighborly Nieuwkerke

New features

1. Added the --min_callable_coverage parameter to state what the lowest coverage should for a region to be classified as callable.
2. Added the elprep caller as an alternative to the haplotypecaller.
3. Added full unit tests for all parts that were missing tests.

Changes

1. Added the --squash-ploidy argument to the RTG vcfeval process.
2. Update to nf-core v3.0.1
3. Completely reworked the output directory structure to a more sensible structure. The pipeline can now be run on the same output directory every time and will incrementally add files to the correct family folder. See the output documentation for more info.
4. Migrated to the new workflow output definitions.
5. Bumped the minimal Nextflow version to 24.10.0.
6. Added the somalier reports to the multiQC report.
7. Removed the --output_suffix parameter
8. Added some missing required parameters to the WES and seqplorer profiles

Fixes

1. Validation of all samples now uses an intersect of the golden truth BED files with the BED file used to call the variants. This should fix the WES validation which was broken until this point.
2. A couple of small fixes to the vardict flow.
3. Only use the standard chromosomes for UPDio analysis.
4. Reduced the resources given to some GATK4 modules
5. VCF2DB now uses a seqera container to fix some issues when running it in nomad
6. Dots in sample and family names are now converted to an underscore automatically.

v1.8.2 - Outstanding Oostkamp

Fixes

1. Fixed some issues where indices were not created
2. Updated the docs

v1.8.1 - Open Oostkamp

Fixes

1. Revert VEP version to v105

v1.8.0 - Optimistic Oostkamp

New features

1. Added watchpath functionality to the pipeline. Add the watch: prefix to a file basename in the samplesheet and the pipeline will automatically wait for the file to be created in the --watchdir directory (the lookup happens recursively)

Changes

1. Bumped the minimal support nextflow version to 24.04.0
2. Bumped all modules to the newest versions
3. The pipeline now also outputs csi indices
4. Rename the master branch to main
5. Low coverage regions (regions with less than 5 reads) are no longer considered for variant calling

Refactors

1. Updated the pipeline to the new linting guidelines
2. Removed check_max in favor of resourceLimits

v1.7.0 - Tolerant Tongeren

Fixes

1. Automap analysis should now give the correct output files for individuals.

Changes

1. Haplotypecaller will not perform phasing by default now. This can still be turned back on using the --hc_phasing parameter.
2. Removed the WES and WGS profiles.

v1.6.0 - Offbeat Ostend

New features

1. Added UPDio for Uniparental Disomy detection in family samples. This introduces the --updio parameter to turn on this detection and --updio_common_cnvs to supply a common CNVs file to UPDio. The family needs to contain at least one child with its mother and father.
2. Added docs built with MkDocs. See the documentation site here.
3. Added AutoMap to find regions of homozygosity from human samples. This introduces the --automap parameter to turn on this feature and the --automap_repeats, --automap_panel and --automap_panel_name parameters to configure AutoMap (see the parameters docs for more information)

Changes

1. Updated all tests to use snapshots instead.
2. Made the pipeline pluggable to enable the use of it in a meta pipeline.

v1.5.1 - Great Geraardsbergen

v1.5.1 - Great Geraardsbergen - [March 7 2024]

Fixes

1. Fixed an issue with igenomes paths not being casted correctly to their corresponding parameter

v1.5.0 - Amazing Antwerp

Improvements

1. Updated to the nf-core template v2.13.0
2. Updated all GATK modules to 4.5.0.0
3. Moved the pipeline from https://github.com/CenterForMedicalGeneticsGhent/nf-cmgg-germline to https://github.com/nf-cmgg/germline

Changes

1. VCF files created with haplotypecaller now have the haplotypecaller tag in the filename instead of gatk4-joint to keep naming consistent

v1.4.2 - Vibrant Veurne

Fixes

1. Set the default ensembl VEP version to 105.0 instead of using dynamic container fetching